Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape

The use of scat surveys to obtain DNA has been well documented in temperate areas, where DNA preservation may be more effective than in tropical forests. Samples obtained in the tropics are often exposed to high humidity, warm temperatures, frequent rain and intense sunlight, all of which can rapidly degrade DNA. Despite these potential problems, we demonstrate successful mtDNA amplification and sequencing for faeces of carnivores collected in tropical conditions and quantify how sample condition and environmental variables influence the success of PCR amplification and species identification. Additionally, the feasibility of genotyping nuclear microsatellites from jaguar (Panthera onca) faeces was investigated. From October 2007 to December 2008, 93 faecal samples were collected in the southern Brazilian Amazon. A total of eight carnivore species was successfully identified from 71% of all samples obtained. Information theoretic analysis revealed that the number of PCR attempts before a successful sequence was an important negative predictor across all three responses (success of species identification, success of species identification from the first sequence and PCR amplification success), whereas the relative importance of the other three predictors (sample condition, season and distance from forest edge) varied between the three responses. Nuclear microsatellite amplification from jaguar faeces had lower success rates (15-44%) compared with those of the mtDNA marker. Our results show that DNA obtained from faecal samples works efficiently for carnivore species identification in the Amazon forest and also shows potential for nuclear DNA analysis, thus providing a valuable tool for genetic, ecological and conservation studies.

Toward a resolution of Campanulid phylogeny, with special reference to the placement of Dipsacales

Broad-scale phylogenetic analyses of the angiosperms and of the Asteridae have failed to confidently resolve relationships among the major lineages of the campanulid Asteridae (i.e., the euasterid II of APG II, 2003). To address this problem we assembled presently available sequences for a core set of 50 taxa, representing the diversity of the four largest lineages (Apiales, Aquifoliales, Asterales, Dipsacales) as well as the smaller ""unplaced"" groups (e.g., Bruniaceae, Paracryphiaceae, Columelliaceae). We constructed four data matrices for phylogenetic analysis: a chloroplast coding matrix (atpB, matK, ndhF, rbcL), a chloroplast non-coding matrix (rps16 intron, trnT-F region, trnV-atpE IGS), a combined chloroplast dataset (all seven chloroplast regions), and a combined genome matrix (seven chloroplast regions plus 18S and 26S rDNA). Bayesian analyses of these datasets using mixed substitution models produced often well-resolved and supported trees. Consistent with more weakly supported results from previous studies, our analyses support the monophyly of the four major clades and the relationships among them. Most importantly, Asterales are inferred to be sister to a clade containing Apiales and Dipsacales. Paracryphiaceae is consistently placed sister to the Dipsacales. However, the exact relationships of Bruniaceae, Columelliaceae, and an Escallonia clade depended upon the dataset. Areas of poor resolution in combined analyses may be partly explained by conflict between the coding and non-coding data partitions. We discuss the implications of these results for our understanding of campanulid phylogeny and evolution, paying special attention to how our findings bear on character evolution and biogeography in Dipsacales.

Cearania heterophylla gen. nov et sp nov., a fossil gymnosperm with affinities to the Gnetales from the Early Cretaceous of northern Gondwana

Vegetative and fertile shoots of a shrub-like seed plant from the late Aptian Crato Formation of Brazil are described as Cearania heterophylla Kunzmann, Mohr and Bernardes-de-Oliveira, gen. nov. et sp. nov. Anatomical details of the axes, epidermal features and separate ovulate and pollen producing organs indicate the gymnospermous nature of this plant. The vascular tissue of the axes includes tracheids with bordered pits and fiber tracheids. Vegetative shoots comprising at least three branching orders bear opposite-decussately arranged ovate to lanceolate, dorsiventrally flattened, parallelodromous, rather thick leaves that vary tremendously in size. The amphistomatic leaves bear (brachy-)paracytic stomatal complexes arranged in simple longitudinal files. The ovulate structure is interpreted as a terminally attached single globular ovule/seed surrounded by at least five to six lanceolate bracts. A terminally attached pollen-cone like structure grows on a lateral leafy shoot. The unusual character combination may indicate that the fossils belong to a hitherto unknown group with affinities to ephedroid Gnetales. Sterile shoots formerly often described as Podozamites, Nageiopsis or Lilites that are at least partly congeneric with C. heterophylla Kunzmann, Mohr and Bernardes-de-Oliveira, gen. nov. et sp. nov. had a wide geographic distribution during the Early Cretaceous. (C) 2009 Elsevier B.V. All rights reserved.